Root zone N management can reduce N fertilizer input and avoid nitrate pollution in greenhouse tomato production; however, little information is available on how reduced N affects soil microbes, especially dominant bacteria populations in long-term continuous greenhouse systems. This study investigated the effects of different combinations of N and straw on the population size of soil total bacteria and two dominant bacteria (Pseudomonas spp. and Bacillus spp.), and microbial community structure in a 6-year greenhouse tomato trial. The treatments were basal fertilizer (10 t ha^-1 chicken manure; control), conventional high N treatment [600 kg N ha^-1], conventional high N treatment with wheat straw, reduced N treatment [300 kg N ha^-1 less than conventional], and reduced N treatment with wheat straw. Six years of reduced mineral N fertilization did not lead to a decrease in fruit yield. Both mineral N fertilizer and straw increased the numbers of soil bacteria (Bacillus spp. and Pseudomonas spp.) compared with the control, but the numbers were not affected by the amount of mineral N fertilizer (high vs reduced). Different denaturing gradient gel electrophoresis patterns were evidence that soil bacterial communities were changed by N treatments and straw application, but little difference in bacterial diversity was detected between high N and reduced N treatments. These results indicated that a reduction in N fertilizer input was possible in greenhouse tomato production and was beneficial in sustainable agriculture.